Single cell and multi-omics analysis reveal senescence-related molecular subtypes and a prognostic signature in clear cell renal cell carcinoma

Clear cell renal cell carcinoma (ccRCC) is the most prevalent subtype of renal cancer and represents high heterogeneity and poor prognosis. Current evidence highlights that the senescence program, particularly through SASP, can simultaneously impose tumor-suppressive barriers and, under specific conditions, support malignant progression. Nevertheless, the comprehensive characterization and clinical significance of cellular senescence in ccRCC have yet to be fully elucidated.

We integrated single-cell and bulk transcriptomic data to characterize senescence-associated features in ccRCC. Single-cell RNA sequencing (scRNA-seq) data from normal, peritumoral, and tumor tissues (GSE222703 and GSE210042) were used to assess SASP signatures across cell types. Differentially expressed senescence-associated genes (SAGs) were identified from TCGA-KIRC and used for consensus clustering. A risk score model was constructed using Random Survival Forest (RSF) based on key SAGs and validated across three independent cohorts [TCGA-KIRC (n = 537), E-MTAB-1980 (n = 101), and CPTAC-ccRCC (n = 105)]. Immune cell infiltration, clinical associations, and prognostic utility were further evaluated. A nomogram was developed and tested for survival prediction.

Senescence signatures were enriched in epithelial tumor cells, especially in ccRCC tissues compared to normal and peritumoral tissues. Two distinct molecular subtypes (C1 and C2) were defined by SAG expression, with C1 exhibiting stronger senescence activity and better survival outcomes. The RSF-based risk score showed robust performance across all cohorts and was independently associated with survival. High-risk patients displayed lower immune activation, reduced antigen presentation, and a more immunosuppressive microenvironment. A survival nomogram integrating the risk score with clinical parameters achieved high predictive accuracy. Among all SAGs, ALDH18A1 was identified as a key prognostic gene and was significantly upregulated in ccRCC. In addition, single-cell sequencing analysis revealed substantial interactions between ALDH18A1⁺ tumor cells and components of the immune microenvironment. Subsequently, tissue and cell line validation indicated a high expression of ALDH18A1 in ccRCC. Experimental validation demonstrated that ALDH18A1 is functionally involved in promoting ccRCC cell proliferation.

In this study, we uncovered the diverse patterns of cellular senescence within ccRCC and developed a senescence-derived risk score that demonstrated strong prognostic value. Moreover, ALDH18A1 was identified as a promising biomarker for prognosis and a potential therapeutic target in ccRCC.